| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Accuracy (OncoKB benchmark (positive set not stated), default categorical calls) | 0.66 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls) | 0.85 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Precision (OncoKB benchmark (positive set not stated), default categorical calls) | 0.6 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Specificity (OncoKB benchmark (positive set not stated), default categorical calls) | 0.39 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Accuracy (OncoKB benchmark (positive set not stated), median-score threshold) | 0.65 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Negative predictive value (OncoKB benchmark (positive set not stated), median-score threshold) | 0.65 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Precision (OncoKB benchmark (positive set not stated), median-score threshold) | 0.65 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Recall (OncoKB benchmark (positive set not stated), median-score threshold) | 0.65 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | FATHMM-XF (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Specificity (OncoKB benchmark (positive set not stated), median-score threshold) | 0.65 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, default categorical calls (Chen et al. 2020 Additional file 22) | Negative predictive value (cell viability drivers versus neutral, default categorical calls) | 0.72 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, default categorical calls (Chen et al. 2020 Additional file 22) | Recall (cell viability drivers versus neutral, default categorical calls) | 0.89 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, default categorical calls (Chen et al. 2020 Additional file 22) | Specificity (cell viability drivers versus neutral, default categorical calls) | 0.28 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Accuracy (cell viability drivers versus neutral, median-score threshold) | 0.63 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Negative predictive value (cell viability drivers versus neutral, median-score threshold) | 0.63 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Precision (cell viability drivers versus neutral, median-score threshold) | 0.63 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Recall (cell viability drivers versus neutral, median-score threshold) | 0.63 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | FATHMM-XF (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Specificity (cell viability drivers versus neutral, median-score threshold) | 0.63 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Accuracy (OncoKB benchmark (positive set not stated), default categorical calls) | 0.62 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls) | 0.79 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Precision (OncoKB benchmark (positive set not stated), default categorical calls) | 0.58 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) | Specificity (OncoKB benchmark (positive set not stated), default categorical calls) | 0.29 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Accuracy (OncoKB benchmark (positive set not stated), median-score threshold) | 0.63 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Negative predictive value (OncoKB benchmark (positive set not stated), median-score threshold) | 0.63 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Precision (OncoKB benchmark (positive set not stated), median-score threshold) | 0.62 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Recall (OncoKB benchmark (positive set not stated), median-score threshold) | 0.64 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) | Polyphen2_HDIV (Chen et al. 2020) | OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) | Specificity (OncoKB benchmark (positive set not stated), median-score threshold) | 0.62 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, default categorical calls (Chen et al. 2020 Additional file 22) | Negative predictive value (cell viability drivers versus neutral, default categorical calls) | 0.7 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, default categorical calls (Chen et al. 2020 Additional file 22) | Recall (cell viability drivers versus neutral, default categorical calls) | 0.88 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 22: Performance metrics of 17 algorithms, default categories, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, default categorical calls (Chen et al. 2020 Additional file 22) | Specificity (cell viability drivers versus neutral, default categorical calls) | 0.29 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Accuracy (cell viability drivers versus neutral, median-score threshold) | 0.58 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Negative predictive value (cell viability drivers versus neutral, median-score threshold) | 0.58 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Precision (cell viability drivers versus neutral, median-score threshold) | 0.58 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Recall (cell viability drivers versus neutral, median-score threshold) | 0.58 |
|---|
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) | Polyphen2_HDIV (Chen et al. 2020) | Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) | Specificity (cell viability drivers versus neutral, median-score threshold) | 0.57 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv) | Average precision (CGC missense, all genes) | 0.568 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) | Average precision (CGC missense, oncogenes (gain of function)) | 0.644 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) | Average precision (CGC missense, tumour suppressors (loss of function)) | 0.476 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | fathmm-XF_coding rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) | AUROC (CGC missense, tumour suppressors (loss of function)) | 0.857 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | Polyphen2_HDIV rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, all genes (Lee 2026, OncoCal tool_performance.tsv) | Average precision (CGC missense, all genes) | 0.47 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | Polyphen2_HDIV rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, oncogenes (gain of function) (Lee 2026, OncoCal tool_performance.tsv) | Average precision (CGC missense, oncogenes (gain of function)) | 0.541 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | Polyphen2_HDIV rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) | Average precision (CGC missense, tumour suppressors (loss of function)) | 0.409 |
|---|
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers; OncoCal repository, tables/tool_performance.tsv (per-tool AUROC and AUPRC by gene role) | Polyphen2_HDIV rank score, dbNSFP 5.3.1a (Lee 2026) | CGC missense oncogenicity, tumour suppressors (loss of function) (Lee 2026, OncoCal tool_performance.tsv) | AUROC (CGC missense, tumour suppressors (loss of function)) | 0.847 |
|---|